Because the shirt/pants color thing was more or less a feature of the renderer in software quake: it could dynamically recolor the shirt/pants palette colors as it drew to the screen.
Under GLQuake, all the graphics need to be upsampled to 32 bit images and cannot simply be recolored on render, as the textures need to be uploaded to their final state to the video card. As a hack, one texture (a version of the player.mdl skin) is uploaded to the video card for each client on the server. That alone is not much of a problem - except for the fact it prevents recoloring of other models if, for example, the player can morph - the major problem arises that whoever programmed this system neglected to even look at the colormap value. Rather than referencing the colormap to assign the appropriate texture for each client, it instead uses their entity number directly to find that client's texture. This breaks the primary use of colormap, namely showing the correct colors on dead bodies and further prevents us bot coders from using it to display the correct client colors on our bots. This is why this 'feature' is listed on QIP.